diff --git a/CHANGELOG.md b/CHANGELOG.md index 0062af4..eb520ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,9 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI. - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests +- [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation +- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline +- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md ### `Fixed` diff --git a/README.md b/README.md index 6cf36dc..29e031d 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ ## Introduction -**nf-core/seqinspector** is a bioinformatics pipeline that ... +**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencing data to provide comprehensive quality control and exploratory analysis. It performs subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed reports with flexible output options, ranging from individual sample analyses to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. - 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk)) 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2)) +4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)) +5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage diff --git a/conf/test.config b/conf/test.config index 0ebc405..1b222be 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,8 +23,6 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv' fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"